From 6476f5f49b373cd4cf05f2e73389df83e437d597 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 16:30:31 +0100 Subject: Axis legend formatting, update vignettes --- docs/dev/articles/web_only/benchmarks.html | 1002 ---------------------------- 1 file changed, 1002 deletions(-) delete mode 100644 docs/dev/articles/web_only/benchmarks.html (limited to 'docs/dev/articles/web_only/benchmarks.html') diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html deleted file mode 100644 index 87bdd55f..00000000 --- a/docs/dev/articles/web_only/benchmarks.html +++ /dev/null @@ -1,1002 +0,0 @@ - - - - - - - -Benchmark timings for mkin • mkin - - - - - - - - - - - - - -
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Benchmark timings for mkin

-

Johannes -Ranke

- -

Last change 17 February 2023 -(rebuilt 2023-04-16)

- - Source: vignettes/web_only/benchmarks.rmd - - -
- - - -

Each system is characterized by the operating system type, the CPU -type, the mkin version, and, as in June 2022 the current R version lead -to worse performance, the R version. A compiler was available, so if no -analytical solution was available, compiled ODE models are used.

-

Every fit is only performed once, so the accuracy of the benchmarks -is limited.

-

The following wrapper function for mmkin is used because -the way the error model is specified was changed in mkin version -0.9.49.1.

-
-if (packageVersion("mkin") > "0.9.48.1") {
-  mmkin_bench <- function(models, datasets, error_model = "const") {
-    mmkin(models, datasets, error_model = error_model, cores = 1, quiet = TRUE)
-  }
-} else {
-  mmkin_bench <- function(models, datasets, error_model = NULL) {
-    mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE)
-  }
-}
-
-

Test cases -

-

Parent only:

-
-FOCUS_C <- FOCUS_2006_C
-FOCUS_D <- subset(FOCUS_2006_D, value != 0)
-parent_datasets <- list(FOCUS_C, FOCUS_D)
-
-
-t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), parent_datasets))[["elapsed"]]
-t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), parent_datasets,
-    error_model = "tc"))[["elapsed"]]
-

One metabolite:

-
-SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
-FOMC_SFO <- mkinmod(
-  parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub("SFO"))
-DFOP_SFO <- mkinmod(
-  parent = mkinsub("FOMC", "m1"), # erroneously used FOMC twice, not fixed for consistency
-  m1 = mkinsub("SFO"))
-t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[["elapsed"]]
-t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
-    error_model = "tc"))[["elapsed"]]
-t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
-    error_model = "obs"))[["elapsed"]]
-

Two metabolites, synthetic data:

-
-m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
-                           M1 = mkinsub("SFO", "M2"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
-
-m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-                           M1 = mkinsub("SFO"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
-
-SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
-
-DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
-
-t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))[["elapsed"]]
-t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[["elapsed"]]
-
-t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
-    error_model = "tc"))[["elapsed"]]
-t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
-    error_model = "tc"))[["elapsed"]]
-
-t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
-    error_model = "obs"))[["elapsed"]]
-t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
-    error_model = "obs"))[["elapsed"]]
-
-
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Results -

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Benchmarks for all available error models are shown. They are -intended for improving mkin, not for comparing CPUs or operating -systems. All trademarks belong to their respective owners.

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Parent only -

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Constant variance (t1) and two-component error model (t2) for four -models fitted to two datasets, i.e. eight fits for each test.

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OSCPURmkint1t2
LinuxRyzen 7 1700NA0.9.48.13.61011.019
LinuxRyzen 7 1700NA0.9.49.18.18422.889
LinuxRyzen 7 1700NA0.9.49.27.06412.558
LinuxRyzen 7 1700NA0.9.49.37.29621.239
LinuxRyzen 7 1700NA0.9.49.45.93620.545
LinuxRyzen 7 1700NA0.9.50.21.7143.971
LinuxRyzen 7 1700NA0.9.50.31.7524.156
LinuxRyzen 7 1700NA0.9.50.41.7863.729
LinuxRyzen 7 1700NA1.0.31.8813.504
LinuxRyzen 7 1700NA1.0.41.8673.450
LinuxRyzen 7 17004.1.31.1.01.7913.289
LinuxRyzen 7 17004.2.11.1.01.8423.453
Linuxi7-4710MQ4.2.11.1.01.9594.116
Linuxi7-4710MQ4.1.31.1.01.8773.906
Linuxi7-4710MQ4.2.11.1.11.6443.172
LinuxRyzen 7 17004.2.11.1.11.7703.377
LinuxRyzen 7 17004.2.11.1.21.9573.633
LinuxRyzen 7 17004.2.21.2.02.1403.774
LinuxRyzen 7 17004.2.21.2.22.1873.851
LinuxRyzen 9 7950X4.2.21.2.01.2881.794
LinuxRyzen 9 7950X4.2.21.2.21.2761.804
LinuxRyzen 9 7950X4.2.21.2.31.3701.883
LinuxRyzen 9 7950X4.2.31.2.31.4041.933
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One metabolite -

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Constant variance (t3), two-component error model (t4), and variance -by variable (t5) for three models fitted to one dataset, i.e. three fits -for each test.

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OSCPURmkint3t4t5
LinuxRyzen 7 1700NA0.9.48.13.76414.3479.495
LinuxRyzen 7 1700NA0.9.49.14.64913.7896.395
LinuxRyzen 7 1700NA0.9.49.24.7868.4615.675
LinuxRyzen 7 1700NA0.9.49.34.51013.8057.386
LinuxRyzen 7 1700NA0.9.49.44.44615.3356.002
LinuxRyzen 7 1700NA0.9.50.21.4026.1742.764
LinuxRyzen 7 1700NA0.9.50.31.4306.6152.878
LinuxRyzen 7 1700NA0.9.50.41.3977.2512.810
LinuxRyzen 7 1700NA1.0.31.4306.3442.798
LinuxRyzen 7 1700NA1.0.41.4156.3642.820
LinuxRyzen 7 17004.1.31.1.01.3106.2792.681
LinuxRyzen 7 17004.2.11.1.03.80221.2478.461
Linuxi7-4710MQ4.2.11.1.03.33419.5217.565
Linuxi7-4710MQ4.1.31.1.01.5788.0583.339
Linuxi7-4710MQ4.2.11.1.11.2305.8392.444
LinuxRyzen 7 17004.2.11.1.11.3085.7582.558
LinuxRyzen 7 17004.2.11.1.21.5036.1472.803
LinuxRyzen 7 17004.2.21.2.01.5546.1932.843
LinuxRyzen 7 17004.2.21.2.21.5856.3353.003
LinuxRyzen 9 7950X4.2.21.2.00.7922.3781.245
LinuxRyzen 9 7950X4.2.21.2.20.7842.3551.233
LinuxRyzen 9 7950X4.2.21.2.30.7702.0111.123
LinuxRyzen 9 7950X4.2.31.2.30.7972.1241.182
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Two metabolites -

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Constant variance (t6 and t7), two-component error model (t8 and t9), -and variance by variable (t10 and t11) for one model fitted to one -dataset, i.e. one fit for each test.

- ------------ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
OSCPURmkint6t7t8t9t10t11
LinuxRyzen 7 1700NA0.9.48.12.6234.5877.52516.6218.57631.267
LinuxRyzen 7 1700NA0.9.49.12.5424.1284.6328.1713.6765.636
LinuxRyzen 7 1700NA0.9.49.22.7234.4784.8627.6183.5795.574
LinuxRyzen 7 1700NA0.9.49.32.6434.3747.02011.1245.3887.365
LinuxRyzen 7 1700NA0.9.49.42.6354.2594.7377.7633.4275.626
LinuxRyzen 7 1700NA0.9.50.20.7771.2361.3322.8722.0692.987
LinuxRyzen 7 1700NA0.9.50.30.8581.2641.3332.9842.1133.073
LinuxRyzen 7 1700NA0.9.50.40.7831.2821.4863.8151.9583.105
LinuxRyzen 7 1700NA1.0.30.7631.2441.4573.0541.9232.839
LinuxRyzen 7 1700NA1.0.40.7851.2521.4663.0911.9362.826
LinuxRyzen 7 17004.1.31.1.00.7441.2271.2883.5531.8952.738
LinuxRyzen 7 17004.2.11.1.03.0184.1655.03610.8446.6239.722
Linuxi7-4710MQ4.2.11.1.02.5223.7924.14311.2685.9358.728
Linuxi7-4710MQ4.1.31.1.00.9071.5351.5894.5442.3023.463
Linuxi7-4710MQ4.2.11.1.10.6781.0951.1493.2471.6582.472
LinuxRyzen 7 17004.2.11.1.10.6961.1241.3212.7861.7442.566
LinuxRyzen 7 17004.2.11.1.20.8611.2951.5073.1021.9612.852
LinuxRyzen 7 17004.2.21.2.00.9131.3451.5393.0111.9872.802
LinuxRyzen 7 17004.2.21.2.20.9351.3811.5513.2091.9763.013
LinuxRyzen 9 7950X4.2.21.2.00.4450.5910.6601.1900.8141.100
LinuxRyzen 9 7950X4.2.21.2.20.4430.5860.6611.1760.8031.097
LinuxRyzen 9 7950X4.2.21.2.30.4180.5300.5911.0060.7160.949
LinuxRyzen 9 7950X4.2.31.2.30.4320.5510.6161.0390.7340.981
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